qlex - I can't duplicate that bug - what conditions are you using it in? (ie; SS version, Simplify version, browser, Simplify permissions selected)
I know the tree had issues in earlier versions of Simplify, but you shouldn't see it in 0.0.6 onwards.
Yes, the Fields tree is designed to hide certain fields and tabs from users. It currently works by doing an AJAX call to the server everytime you click on a checkbox - so use Firebug and look both in the Console and the Net tab - there should be a GET to the server when you click - (admin/simplify/toggleFieldsPermission) - check the response, it should be empty, but it may have an error.
The quickest way for me to debug would be to look at your CMS directly - so if you have a dev or test version (or just copy it) I'm happy to log in and take a look.
Also as to the simplicity philosophy - I agree - I think Silverstripe does have the right idea by building a solid, simple base to work on, and seperating design, development and admin.
If users want more 'stuff' they can get it in modules, like Simplify.